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0
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618
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News: BioC2024 in-person registration closes soon (July 10)
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17 months ago Maria Doyle ▴ 110
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1
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641
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unreal negative log2fc values
DESeq2 des
updated 17 months ago by 68k • written 17 months ago by • 0
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426
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Error in bam loading in getUniqueCleavageEvents() in GUIDEseq package
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17 months ago StayM • 0
0
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0
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1.6k
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Job: Toxicogenomics Statistician
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updated 17 months ago by 4.2k • written 21.6 years ago by ▴ 460
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Spam: GenOMICC DNA biobank
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17 months ago Jolka 0
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1
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686
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Create a Graph w/ Only the Genes Interaction
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17 months ago Antonio • 0
0
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0
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505
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EPIC v2 annotation and BigWig
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17 months ago MajaVu • 0
0
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1
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558
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 17 months ago by 43k • written 17 months ago by • 0
0
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0
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731
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Improving Gene Matching for CIBERSORT Deconvolution with Monaco Reference Matrix in Bulk RNA-Seq
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17 months ago chunglee13 • 0
0
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4
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Trouble Installing DADA2 (warning: R new user)
dada2
updated 17 months ago by 4.2k • written 17 months ago by • 0
0
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721
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Difference in Predictive component of PLS and OPLS Model
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17 months ago devarti.mahakalkar • 0
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0
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720
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Problem with MethylAid ("Cannot get Manifest object for an 'Unknown' array") and Epicv2
minfi EPICv2manifest MethylAid
17 months ago pcibin • 0
0
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4
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9.0k
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Any tools to convert .gff to .gtf format
AnnotationData CrispRdesignR BSgenome
updated 11 months ago by • 0 • written 3.3 years ago by • 0
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3
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963
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Conumee with EPICv2 Segment function
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updated 8 months ago by • 0 • written 17 months ago by • 0
0
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0
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854
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Job: Postdoc Opportunity in Bioinformatics at Northwestern University (Research on Human Pregnancy and Autoimmunity)
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17 months ago Damini • 0
0
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1
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693
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single excel file containing methylation beta values does not get loaded in ChAMP
ChAMP
updated 17 months ago by ▴ 780 • written 17 months ago by • 0
1
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2
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775
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How to get the DMR?
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17 months ago Alex • 0
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389
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Remove Control Probes from Affymetrix Human Gene 1.0 ST Array probeset version
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17 months ago drexjaramel • 0
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3
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993
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How to search Pubmed Central or other fulltext literature base using regex?
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17 months ago Abiologist • 0
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1
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
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updated 17 months ago by • 0 • written 17 months ago by • 0
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499
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Understanding Differentially Abundant Neighbourhood Identification
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17 months ago Dario Strbenac ★ 1.6k
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2
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Unable to install the package "tissuesGeneExpression"
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updated 17 months ago by • 0 • written 8.4 years ago by ▴ 10
1
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13
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Ranking the GSEA Results
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17 months ago • updated 16 months ago V_Vibes • 0
1
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8
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Advice on appropriateness of an offset in glmGamPoi/edgeR
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updated 17 months ago by 53k • written 17 months ago by • 0
0
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2
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Species level information couldn't find with DADA2 bioconductor package
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17 months ago • updated 15 months ago abhisek001 • 0
3
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2.1k
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Difference between enrichGO results and Enrichr website results
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updated 17 months ago by ★ 4.1k • written 17 months ago by ▴ 10
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Risa package missing from Bioconductor 3.19
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updated 17 months ago by 68k • written 17 months ago by • 0
1
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2
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Struggling to convert a large list of non-model genes into human orthologs, any suggestions?
annotation
17 months ago ronin • 0
0
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0
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715
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Cell type deconvolution of RNAseq data- Create signature matrix of cells
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17 months ago JG13 • 0
0
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1
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742
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BiomaRt listAttributes - which are external ?
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updated 17 months ago by 68k • written 17 months ago by • 0
0
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0
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810
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17 months ago gamma.jian ▴ 10
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2
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
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17 months ago sropri • 0
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5
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modelGeneVarByPoisson error selecting bandwidth automatically
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updated 17 months ago by ▴ 760 • written 17 months ago by ▴ 760
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SeSAMe DMR for EPIC V2
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EnsDb: bad_weak_ptr
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17 months ago Lluís Revilla Sancho ▴ 760
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5
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Cannot connect to annotationhub server
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updated 17 months ago by 4.2k • written 17 months ago by • 0
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Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
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17 months ago sukeshinik5 ▴ 20
0
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0
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469
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Structural Variant Format Converted for BRASS Format
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17 months ago Dario Strbenac ★ 1.6k
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1
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569
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Deseq2 design matrix
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updated 17 months ago by 68k • written 17 months ago by • 0
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2
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Issues with retrieving mouse SNP dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
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17 months ago Svitlana ▴ 10
0
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0
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472
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Differential Gene Wrapper for Propotion of Detected
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17 months ago Dario Strbenac ★ 1.6k
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2
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PCA (Principal Component Analysis) plots from ChIP-seq data
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17 months ago egbastakis • 0
4
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4
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1.1k
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Warning message when running limma with covariates
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17 months ago • updated 11 months ago Chris ▴ 20
0
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9
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1.5k
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Research Project - Expanding search funtionality on the GEO database
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17 months ago gallantk5 • 0
3
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5
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Right way to pseudobulk donors across replicates in edgeR
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updated 17 months ago by • 0 • written 21 months ago by ▴ 60
0
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8
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2.2k
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limma comparison for small sample size and how to get covariance matrix
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17 months ago jiachengd • 0
5
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5
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1.7k
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Limma with covariates
limma
written 17 months ago by ▴ 20
1
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1
reply
773
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
0
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2
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Epicv2 conversion fail
minfi
17 months ago Alex • 0
1
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5
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DESeq2 ML Query
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updated 16 months ago by 43k • written 17 months ago by • 0
46,691 results • Page 20 of 934
Recent ...
Replies
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
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